5MB1

STRUCTURE OF THE LECB LECTIN FROM PSEUDOMONAS AERUGINOSA STRAIN PA14 IN COMPLEX WITH 2,4,6-Trimethylphenylsulfonamide-N-methyl-L-fucopyranoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.133 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Glycomimetic, Orally Bioavailable LecB Inhibitors Block Biofilm Formation of Pseudomonas aeruginosa.

Sommer, R.Wagner, S.Rox, K.Varrot, A.Hauck, D.Wamhoff, E.C.Schreiber, J.Ryckmans, T.Brunner, T.Rademacher, C.Hartmann, R.W.Bronstrup, M.Imberty, A.Titz, A.

(2018) J Am Chem Soc 140: 2537-2545

  • DOI: https://doi.org/10.1021/jacs.7b11133
  • Primary Citation of Related Structures:  
    5MAY, 5MB1

  • PubMed Abstract: 

    The opportunistic Gram-negative bacterium Pseudomonas aeruginosa is a leading pathogen for infections of immuno-compromised patients and those suffering from cystic fibrosis. Its ability to switch from planktonic life to aggregates, forming the so-called biofilms, is a front-line mechanism of antimicrobial resistance. The bacterial carbohydrate-binding protein LecB is an integral component and necessary for biofilm formation. Here, we report a new class of drug-like low molecular weight inhibitors of the lectin LecB with nanomolar affinities and excellent receptor binding kinetics and thermodynamics. This class of glycomimetic inhibitors efficiently blocked biofilm formation of P. aeruginosa in vitro while the natural monovalent carbohydrate ligands failed. Furthermore, excellent selectivity and pharmacokinetic properties were achieved. Notably, two compounds showed good oral bioavailability, and high compound concentrations in plasma and urine were achieved in vivo.


  • Organizational Affiliation

    Chemical Biology of Carbohydrates and ‡Drug Design and Development, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) , D-66123 Saarbrücken, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fucose-binding lectin PA-IIL
A, B, C, D
114Pseudomonas aeruginosa UCBPP-PA14Mutation(s): 0 
Gene Names: lecBPA14_20610
UniProt
Find proteins for A0A0H2ZE85 (Pseudomonas aeruginosa (strain UCBPP-PA14))
Explore A0A0H2ZE85 
Go to UniProtKB:  A0A0H2ZE85
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2ZE85
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7KT
Query on 7KT

Download Ideal Coordinates CCD File 
H [auth A],
L [auth B],
Q [auth D]
~{N},2,4,6-tetramethylbenzenesulfonamide
C10 H15 N O2 S
MIMYTDNFDINXHB-UHFFFAOYSA-N
FLC
Query on FLC

Download Ideal Coordinates CCD File 
R [auth D]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
FUL
Query on FUL

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
P [auth D]
beta-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-KGJVWPDLSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
I [auth B]
J [auth B]
M [auth C]
E [auth A],
F [auth A],
I [auth B],
J [auth B],
M [auth C],
N [auth D],
O [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.133 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.904α = 90
b = 65.251β = 90
c = 108.987γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
COSTCOST-STSM-ECOST-STSM-BM1003-240314-042549

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2018-03-14
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary